2015 Winter Project Week

Welcome to the 20th Project week page!

The 20th PROJECT EVENT It was held June 23-27, 2014 at MIT. It recorded 44 registered attendees, who worked on 42 projects. These attendees represented 11 academic sites (Brigham and Women’s Hospital, CNMS, Massachusetts General Hospital, Univ of Utah, Univ of Iowa, Univ of Michigan, Univ of North Carolina at Chapel Hill, Queen’s Univ, Univ Kiel, Imperial College, Robarts) and 4 companies (GE Global Research, Kitware, Koh Young, Isomics Inc).

Note of Remembrance

This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a tribute page to Ferenc for people who want to share their thoughts.

Introduction

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, built using VTK, ITK, CMake, and CDash, and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

Project Week is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include NAC, NCIGT, QIICR, and OCAIRO. The next event in this ongoing series will occur in Barcelona, Spain in June 2015.

A summary of all previous Project Events is available here.

This project week is an event endorsed by the MICCAI society.

Please make sure that you are on the na-mic-project-week mailing list

Logistics

• Dates: January 5-9, 2015.
• Location: Salt Lake City, Utah
• REGISTRATION: Please click here to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
• Venue: The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking here. The room rate for the meeting is 149 USD per night.

Agenda

Time	Monday, January 5	Tuesday, January 6	Wednesday, January 7	Thursday, January 8	Friday, January 9
	Project Activities (Olympus B)	Project Activities (Olympus B)	Project Activities (Olympus B)	Project Activities (Olympus B)	Project Activities (Olympus B)
7:30-8:00		Breakfast (Olympus A)	Breakfast (Olympus A)	Breakfast (Olympus A)	Breakfast (Olympus A)
8:00-10:00		9-10am: Breakout Session: CIP (Raul San Jose) (Amethyst 1)	9-10am: Breakout Session:QIICR and DICOM (Andrey Fedorov, Steve Pieper) (Amethyst 1)	Project Activities (Olympus B)	9am: Project Presentations (Olympus B)
10:00-10:30		Coffee (General area)	Coffee (General area)	Coffee (General area)	Coffee (General area)
10:30-12:00		Neurosurgical Ultrasound Breakout		Project Activities (Olympus B)
12:00-1:00	Lunch (Olympus A)	Lunch (Olympus A)	Lunch (Olympus A)	Lunch (Olympus A)	Boxed Lunch and Adjourn (Olympus A)
1:00-3:00	A tribute to Ferenc Jolesz Project Presentations (Olympus B)		(Olympus B)
3:00-3:30	Coffee (General area)	Coffee (General area)	Coffee (General area)	Coffee (General area)
3:00-5:00		3:15-4pm: Breakout Session: Segmentations (Amethyst 1)	3:15-4pm: Breakout Session: Infrastructure (JC, Steve, Alex, Hans, Raul) (Amethyst 1)	Project Activities (Olympus B)
05:00-07:00				6:00 Optional: Beer at Murphy's (like last year)

Projects

• Template for project pages

Image-Guided Therapy

• Review of data from recent AMIGO US/MR neurosurgery (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
• Tracked ultrasound benchtop experimental system for neurosurgery (Steve Pieper, Jim Miller)
• A modified distance for measuring the similarity between fiber tracts (Ruizhi Liao, Lauren O'Donnell)
• Performance of UKF tractography in edema (Ruizhi Liao, Lauren O'Donnell)
• Workflow for prostate navigation and its components (Peter Behringer, Andriy Fedorov)
• Image-based Needle Detection from MRI (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
• Needle Finder Tutorial (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
• Workflow for percutaneous needle place (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
• Application of consumer virtual reality devices in creating environments for diagnostic radiology (Franklin King, Steve Pieper)
• Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI (Anuja Sharma, Guido Gerig)
• Aortic valve replacement using tracked 3D ultrasound (Adam Rankin)
• Communication Protocol for Optical Tracking with Surface Scan (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

COPD

• SlicerCIP Extension (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
• Lung nodule sizing tool (Raul San Jose)
• Density Inspector (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
• Pulmonary Artery/Aorta measuring tool (Jorge Onieva, Rola Harmouche, German Gonzalez)
• Picasa Snap: tagging your favorite slicer snapshots (Jorge Onieva)
• Feature Extraction on ROIs based on Particles (Raul San Jose, James Ross)
• CIP analysis pipelines in Nipype (Rola Harmouche, James Ross, Alex Yarmakovich)
• Supervised fissure enhancement (James Ross, German Gonzalez, Rola Harmouche)
• Organ detection with OpenCV (German Gonzalez, James Ross, Raul San Jose)

Huntington's Disease

• PREDICT-HD Longitudinal Shape Analysis (Regina EY Kim, James Fishbaugh, Hans Johnson)

CTE

• Measurement and visualization using white matter hierarchies in Slicer (Alexander Yarmarkovich, Lauren O'Donnell)

Lung

• Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan)

QIICR

• Segmentation object and enhanced multiframe object IO in DCMTK and Slicer (Steve, Andrey, Michael)
• T1 mapping for variable flip angle (Artem, Xiao, Andrey)
• Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer, Steve Pieper)
• Whole Body PET/CT Reference Region segmentation (Christian Bauer)
• Bolus Arrival Time (BAT) Estimation in PK Modelling (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
• DICOM Module Improvements (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
• Slice View Annotations (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

Feature Extraction

• 3D SIFT Feature Visualization in Slicer (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
• Experimental tract-based cortical clustering (Lauren O'Donnell, William Wells)

Slicer4 Extensions

• PET Tumor Segmentation (Christian Bauer)

TMJOA RO1 - Collaboration with NAMIC

• Display of point data vectors on Slicer models (Francois Budin, Steve Pieper)

Infrastructure

• Micro and Macro Scale in Slicer (Nicole Aucoin, Jim Miller, Bradley Lowekamp)
• Markups (Nicole Aucoin)
• Segmentations (Csaba Pinter)
• DICOM references (Andrey Fedorov, Csaba Pinter, Steve Pieper)
• Open Atlas (Bill Lorensen)
• Remove ITKv3 Compatibility for 64-bit image support (Bradley Lowekamp, Hans Johnson, Bill Lorensen, JC)
• ITK Composed Versor Transforms (Bradley Lowekamp, Hans Johnson, Jim Miller)

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

1. Nicole Aucoin :: Brigham and Women's Hospital
2. Bamshad Azizi Koutenaei :: Children's National Health System
3. Christian Bauer :: University of Iowa
4. Peter Behringer :: Brigham and Women's Hospital
5. Francois Budin :: University of North Carolina
6. Xiao Da :: Massachusetts General Hospital
7. Andriy Fedorov :: Brigham and Women's Hospital
8. Jean-Christophe Fillion-Robin :: Kitware, Inc.
9. James Fishbaugh :: University of Utah
10. Yang Gao :: Brigham and Women's Hospital
11. German Gonzalez :: Brigham and Women's Hospital
12. Rola Harmouche :: Brigham and Women's Hospital
13. Hans Johnson :: University of Iowa
14. Tina Kapur :: Brigham and Women's Hospital
15. Ron Kikinis :: Brigham and Women's Hospital
16. Eun Young Regina Kim :: University of Iowa
17. Sangyong Kim :: Kohyoung Techonology
18. Franklin King :: Queen's University
19. Byunghyun Cho Koh :: Young Technology Inc.
20. Ming Li :: Brigham and Women's Hospital
21. Ye Li :: Brigham and Women's Hospital
22. Ruizhi Liao :: Brigham and Women's Hospital
23. Julia Lopinto :: University of Michigan
24. Bill Lorensen :: Bill's Basement
25. Bradley Lowekamp :: Medical Science & Computing Inc.
26. Lucie Macron :: University of Michigan
27. Artem Mamonov :: Massachusetts General Hospital
28. Andre Mastmeyer :: University of Keil
29. Alireza Mehrtash :: Brigham and Women's Hospital
30. James Miller :: General Electric
31. Lauren O'Donnell :: Brigham and Women's Hospital
32. Jorge Onieva :: Brigham and Women's Hospital
33. Guillaume Pernelle :: Imperial College London
34. Steve Pieper :: Isomics, Inc.
35. Csaba Pinter :: Queen's University
36. Adam Rankin :: Robarts Research Institute
37. James Ross :: Brigham and Women's Hospital
38. Raul San Jose Estepar :: Brigham and Women's Hospital
39. Anuja Sharma :: University of Utah
40. Matthew Toews :: Brigham and Women's Hospital
41. Junichi Tokuda :: Brigham and Women's Hospital
42. Bo Wang :: University of Utah
43. Sandy Wells :: Brigham and Women's Hospital
44. Alexander Yarmarkovich :: Brigham and Women's Hospital